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Since you are going during Autumn, I can suggest one place to you : Fukuroda Falls. Its a 2-hour train journey from Tokyo Station but its really beautiful. I went there during late Spring, so the leaves were all green, but I can imagine during Autumn, it would be really pretty.
Oh yeah, since you are going during Autumn, the Kyoto Imperial Palace will be open to public for a few days. I am not sure which dates but keep this mind, so that you can be in Kyoto during this time.
Try to pack light. Since laundry services are available is almost all hostels, you can just wash and re-use clothes.
For flights, I can recommend skyscanner.com. The website helped me get cheapest flight to Tokyo.
Accomdation wise, I used booking.com and airbnb. Sometimes, booking.com was cheaper than hostelworld. So, yeah.....
You can also try couchsurfing. I wasn't successful, though.
If you can get the SIM card, do it. But if you can't, get a offline map app. I recommend Maps.me. The Japan maps were accurate and filled with a lot of points of interests like food, cafes and attractions. I used Maps.me together with Google Maps. Also, there is also an offline Japan train app : https://play.google.com/store/apps/details?id=jp.narita_airport.android.tabimori
So, even if you don't have internet access, you can find out which train to take.
Hope this helps in some way.
It is an All in One with a pocket conversation guide, links to japan guide, Currency converter, weather forecast, a transfer guide based on hyperdia, etc.
You can install Tabimori(Android) / Appstore , it's an app that lets you preorder items from the duty free shops at the Narita airport, cigarettes and liquors included!
For a weeb, I would recommend checking out Nakano Broadway. It's this neat multi-floor shopping center filled with all kinds of neat shit. 16 Mandarake stores inside, each with a different specialty like doujinshi, mecha model kits, kaiju stuff, all at a very reasonable price. There were even some small stores with a discount bin that's got some really neat stuff in it for next to nothing. I picked up a TaJaDor Kamen Rider OOO, a Dialga, a Wing Gundam Zero, and a Boss Borot figurine for like 400 yen total. And even if you don't buy much, their displays are pretty great to look at. Especially the one place that had Revoltech Woody. It's beautiful.
You go through Nakano Sun Plaza to get to it, and on your way there, there's this great bakery called Bonjour Bon. They had a really delicious crunchy chocolate melonpan last time I went there. I'd highly recommend getting something there.
If you're into Kamen Rider, Kamen Rider The Diner in Ikebukurou is fantastic. Stop by there after visiting the Pokemon Center. They have a good English Menu, stuff from the shows all over the diner, and lots cool dishes based off the riders. I got the Fourze Parfait as my dessert when I was there, and when it arrived they played his Henshin theme countdown and had me yell "PARFAIT KITAAAAA!!! Sounds silly, but it was so much fun. And protip: DO NOT ORDER NAOMI'S COFFEE. IT TASTES LIKE FOOD COLORING AND YOU WILL POOP BLUE FOR MULTIPLE DAYS.
If you're taking the Shinkansen to Kyoto, make sure you visit Fushimi Inari Shrine. In the two weeks I was there, that was the absolute highlight of my trip. At the base of the mountain before you go in the shrine, there's a ton of outdoor food stalls selling delicious Japanese treats and foods made fresh right before your eyes. I strongly recommend the taiyaki. Piping hot and filled with yummy cream for only 150 yen. The yaki dango was great too, as are the yakitori, karaage, and wagyu beef skewers. You pretty much can't go wrong there.
When you start walking up Mt. Inari, fair warning. Like everything else in Japan, it's a lot of walking. I hope you're in decent shape, or at least fairly determined. I was about 240 but I started running a few months before my trip so I only died a little. I recommend getting an omikuji, then proceeding up on the right path around through the Senbon Torii. A lot of people suggest making it to the area marked "Crossroads" and then heading back down the other path, because I hear there's not much new after that. It's what I did, although you want to head up a little bit past them to get to a gorgeous view ahead where you can look out at Kyoto from about halfway up the mountain.
And while you're in the kansai region, Nara Deer Park is a real treat. Those deer are adorable, but their temperement varies. A few will let you touch them while you're feeding them, but most won't. And some will harass you and bite you right on the ass. I think those deer are the inspiration for The Ring, because the only way to get rid of them is to lead them towards another group.
Anyway, to help you get around, here's the apps I used.
Tabimori has a useful phrase book and general cultural information guide. The currency converter is also pretty helpful if you don't have the exchange rate internalized.
Japanese by Spacehamster is an incredibly detailed and quick translation app for looking up individual words. To translate longer phrases, the Google Translate app works nicely. It also lets you take pictures of Japanese text and translate them that way in case there's stuff you can't read.
For travel, Google Maps or Japan Trains is good for getting from point A to Point B. But it can sometimes be hard to figure out which direction a train is going, so be mindful of that and pay attention to make sure you're not going the wrong way.
For food, Gurunavi is fantastic. You can sort restaurants by type, price, english accommodation etc. It's very useful. Try to find a good Tonkatsu place if you can. 1,650 yen for that rōsu katsu meal set (Miso soup is in the bowl) and it was probably the best thing I ate while I was there.
And on one final note. If you uh, have any interest in ahem quality japanese adult graphic novels, I believe the best place I found was called Melonbooks in Akihabara. It's a bit hard to see the entrance, the sign isn't on the street so you have to go in and then go down the stairs into the basement where all the good stuff is. I believe they're the ones that have sample pages available, which is good for making sure you don't bring home something that might not be legal. Or that you don't accidentally buy vore manga.^Thanks ^for ^nothing, ^Mandarake's ^doujin ^section ^in ^Akihabara.